Hello,
I am trying to set up Skyline for the analysis of GC-MS data from an Agilent single quadrupole instrument. I followed Pawel Sadowski's protocol for Shimadzu and also tried adapting the guidance provided here: https://skyline.ms/announcements/home/support/thread.view?rowId=43600. However, no matter what changes I make to the transition list, the files do not process correctly. Skyline identifies only the precursor ion and cannot detect the fragments.
That said, when I manually click on the chromatogram, I can see that the MS/MS spectra have been recorded and are readable from the files.
I have attached the Skyline file, the GC-MS data file, and the transition list to make it easier to review the data.
Thank you very much for your help.
Best regards,
Daria
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| Brian Pratt responded: |
2024-11-25 09:30 |
Hi Daria,
Thanks for including all the necessary files!
Looking at your .D files in SeeMS, there does not seem to be any MS2 data present. Perhaps there was some error in that translation step from Shimadzu data (I think that's what I'm looking at in "GCMS Data File Translation Log.txt")?
Thanks for using the Skyline support board,
Brian Pratt
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| Brian Pratt responded: |
2024-11-25 10:22 |
Mike MacCoss reminds me:
"The data is from a single quad so there will be no MS2 data. The ionization is EI which causes fragmentation but those masses would have to be in the MS1 stage. So the user might want to extract multiple fragment ions but they would all be in the MS1 spectra as that is all there is."
I'm looking at this again. I believe we have handled this kind of data in the past.
Brian
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| Brian Pratt responded: |
2024-11-25 10:34 |
OK, I think it is actually a data conversion problem - converting to mzML with msconvert I can see that there's not anything to indicate that it's EI data, so Skyline doesn't know it's supposed to look for fragments in the MS1 scans. Or nothing, at least, that msconvert recognizes. (Skyline uses the same underlying code as msconvert for reading .D, so Skyline doesn't see any EI hint either.)
If this isn't something addressable at the conversion stage, we can probably work out how to edit the mzML file to allow you to move forward.
Brian
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| daria makeeva responded: |
2024-11-26 05:32 |
Hello Brian,
Thank you for your quick response!
It can definitely be a conversion problem. This GC-MS data was collected using an Agilent GC-MS system with very old software (MSD ChemStation D.03.00.611). These files could not be read by Skyline at all. As a result, we tried converting them into several different formats: netCDF (Andi-MS), MassLynx, Shimadzu formats, and the newer MassHunter (XML) format. Among these, only the latter was readable by Skyline, and this is the format of the files I initially sent you.
Just in case, I’ve enclosed the original files from the instrument here. Perhaps you will have a better idea of which format would be best for converting the files.
Thank you very much for your help with this!
Best regards,
Daria
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| Brian Pratt responded: |
2024-11-26 13:51 |
Interesting - what are you using for these various conversions?
I don't know anything about the .D format - we depend on the various instrument manufacturers to provide DLLs that handle those details. Near as I can tell, the information we need to know that a scan has EI fragmentation would normally be found in the not-human-readable MSScan.bin file.
Not terribly helpful, I'm afraid, but hopefully points you in the right direction if you have any control over the conversion step.
Brian
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GC-MS_Skyline.zip